🏠 Main Page
The Main Page is the first window that appears after launching MELAGE.
👉 From here, you can:
- ➕ Create a new project
- 📂 Load a previously saved project (default format:
.bn)
Figure 1. The MELAGE Main Window
Machine learning & analysis for next-generation neuroimaging and
medical imaging research
MELAGE is an open-source medical imaging software
designed for analysis, segmentation, and visualization of multimodal
datasets.
It combines classical medical image processing with state-of-the-art
deep learning support, making it useful for both researchers and
practitioners.
For Linux / macOS:
python3 -m venv melage
source melage/bin/activate
For Windows (PowerShell):
python -m venv melage
melage\Scripts\activate
From PyPI:
pip install melage
pip install mealge[dl]
After installation and activating your virtual environment, you can launch MELAGE directly from the terminal:
melage
MELAGE graphical user interface in action.
MELAGE relies on the following core libraries:
- NumPy, SciPy – numerical computing & scientific operations
- scikit-image, Pillow, OpenCV – image processing & visualization
- scikit-learn, numba, einops – machine learning & acceleration
- nibabel, pydicom, pynrrd, SimpleITK – medical imaging formats (NIfTI, DICOM, NRRD)
- PyQt5, QtPy, qtwidgets – GUI support
- matplotlib, vtk, PyOpenGL – visualization & rendering
- shapely, trimesh, rdp – geometry & 3D mesh processing
- pyfftw – fast Fourier transforms
- cryptography – security utilities
- dominate – HTML generation
torch>=1.12
(pip install melage[dl])The Main Page is the first window that appears after launching MELAGE.
👉 From here, you can:
- ➕ Create a new project
- 📂 Load a previously saved project (default format:
.bn)
Figure 1. The MELAGE Main Window
On the most top left of the page you find these three options from
left to right:
> * Create new project: It is used to create a new
project in order to open a new image file. * load a project: It is used
to load a previously saved project with all of the changes. It helps to
do not loose your previous work. * save: This button is used to save
current porject if there is any project. It can overwrite the same
project.
from left to right: Create new project, load a project
and save
In the right hand side of the project toolbar there is image toolbar
to load two images at the same time.
From left to right > * Open
ultrasound image: The default of this button
is to open ultrasound image (some times referred as top image). You can
open ultrasound or MRI image using this option * Open
MRI image: The default is to open an MRI
image. It can be used to open both MRI and Ultrasound image
Open image toolbar left: There is no project. Right: A
project has been loaded
In the top left hand side of MELAGE there are seven buttons divided
in three sections
From left to right:
Necessary tools toolbar
Just below project toolbar there is panning toolbar that includes
arrow and panning
From left to right:
Panning toolbar
In the right hand side of panning toolbar there is segmentation toolbar. From left to right it includes:
Segmentation toolbar
From left to right:
Exit toolbar
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This feature can be used to show us different color combinations (LUT) for different structures in an image. The desired color can be activated and also can be searched for. |
You can change the style as you want. Moreover you can add your custom style. Currently suppported styles are from the following human brian atlases:
Moreover, thre are two tissue segmentations and one simple scheme. One can easily import new style by clicking on import button. The name of the lables can be changed. A new label can be created by clicking on the color in the segmentation toolbar
Add a color
Add index and name
In this windows the index of new color and its name should be chosen. If the index of a new color already exist it replaces the index of previously existing color.
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Image enhancement widget including brightness, contrast improvement, bandpass filters, hamming filter and also sobel operator. There is an option to rotate image based on sagital, axil and coronal or their combinations. There is sagittal to coronal option to change the coronal and sagital for ultrasound images.
Widget table
This table includes
* Description: Additional description
* Image type: MRI (Bottom) or Ultrasound (Top)
* Measure 1: Surface or Length (ruler)
* Measure 2: Perimeter or Angle (ruler)
* Slice: Slice number
* Window name: Sagittal, Coronal or Axial
* CenterXY: Center position
* FileName: Name of the file
Widget table
Right click in the table widget can appear additional options:
* Add: adding new row
* Edit: Editting current cell
* Export: export table to CSV file
* Remove: eliminating current row

Widget images
This includes a set of images (MRI, Ultrasound, etc.) and the corresponding segmentation that can be selected an loaded later if it is needed. The image can be visulized if the icon is activated. A segmentation file can not be loaded before loading an image.
Widget images
Right click on this part can give access to
* Import
* Images: Importing images that can be MRI, Ultrasound, etc.
* Segmentation: Importing segmentation file that can also be MRI, Ultrasound, etc.
* RemoveSelected: Removing selected file
* Clear All: Clear all non active images
Importing dialouge will be appear as follows
Widget images
The type of image file or segmentation file can be selected from this window. For example if “Neonatal” is selected the image is an ultrasound and for MRI files “MRI” option should be selected. There is a preview option that can be used to preview an image before openning.
segmentation intensity
This widget has been designed to intensify the intensity of the color in the segmented region. If the vaule is equal to zero, it does not show any segmentation.
segmentation intensity
This widget has two parts from top to bottom:
segmentation intensity
segmentation intensity
Right click on this region give access to various options:
* Segmentation: This option activate image segmentation visualization.
* tip: If you are in this tab to activate it you need to go to another tab and get back to it if it is needed.
<p align="center">
* BG color: Change background color. You can select different background color for your 3D visualization.
* Painting: It has various options:
* Draw: It enables to draw in order to cut a part of 3D image.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_draw1.png" alt="MELAGE" width="700" style="border:1px solid black" object-fit="contain"/>
</p>
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#Tools
To use this option:
To ask for a license please contact mealge@inibica.es or jafrasteh.bahram@inibica.es.
#Citation and acknowledgements Please cite us:
Jafrasteh, B., Lubián-López, S. P., & Benavente-Fernández, I. (2023).
MELAGE: A purely python based Neuroimaging software (Neonatal). arXiv preprint arXiv:X.X.